Contacts of the strand formed by residues 82 - 86 (chain F) in PDB entry 2GOO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44F THR* 2.7 26.2 + - - -
45F TRP* 2.8 58.9 + + + +
46F LYS* 4.5 1.1 - - - -
47F ASN* 3.4 38.3 + - + +
74F GLU* 3.3 17.9 - - + +
78F SER* 4.3 7.6 + - - -
79F PRO* 3.4 37.3 + - + +
80F GLU 4.7 1.8 - - - -
81F VAL* 1.3 72.8 - - - +
83F PHE* 1.3 55.9 + - - +
97F TYR* 3.5 37.7 + + - -
401F NDG 3.6 20.3 + - + -
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Residues in contact with PHE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 4.0 17.9 - - + +
34D ALA* 3.7 27.6 - - + -
90D LEU* 3.4 30.5 - - + -
42F PHE* 3.6 22.2 - + + -
43F ALA 3.4 10.5 - - - -
45F TRP* 4.2 3.8 - - - -
60F TRP* 3.9 17.9 - + - -
63F ASP* 6.0 0.4 - - - -
65F ASN* 6.5 0.2 - - + -
73F ILE 4.4 0.3 - - - +
74F GLU* 2.7 34.8 + - - +
76F LYS* 6.4 1.6 - - - -
81F VAL 4.8 0.9 - - - +
82F TYR* 1.3 75.8 - - - +
84F CYS* 1.3 73.9 + - - +
85F CYS* 3.8 29.8 - - + -
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Residues in contact with CYS 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PHE* 3.2 5.5 - - - +
43F ALA* 2.9 35.2 + - - +
45F TRP* 3.7 20.9 - - - -
72F CYS* 2.0 52.5 - - - -
73F ILE 3.4 29.4 - - - +
74F GLU 3.9 0.7 - - - +
83F PHE* 1.3 82.7 - - - +
85F CYS* 1.3 60.6 + - - +
95F PHE* 3.7 4.3 - - - -
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Residues in contact with CYS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F CYS 3.1 13.7 - - - +
42F PHE* 4.2 3.4 - - + -
60F TRP* 4.4 4.9 - - + -
63F ASP* 4.9 0.7 - - - -
65F ASN* 4.1 10.1 - - - -
66F CYS* 2.1 51.6 - - - -
69F ARG* 4.1 17.8 - - - +
71F ASP 4.3 3.3 - - - +
72F CYS* 4.1 2.7 - - - -
73F ILE 5.3 0.5 + - - -
83F PHE* 3.8 24.0 - - + -
84F CYS* 1.3 76.3 - - - +
86F CYS* 1.3 64.4 + - - +
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Residues in contact with CYS 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F HIS* 3.2 10.3 - - - +
41F CYS* 2.9 35.5 + - - -
66F CYS* 4.1 3.8 - - - +
69F ARG* 3.1 17.7 - - - +
70F THR 4.4 0.2 - - - -
71F ASP 3.7 16.2 - - - +
72F CYS* 4.0 11.0 - - - -
85F CYS* 1.3 77.1 - - - +
87F GLU* 1.3 63.1 + - - +
91F CYS* 2.1 59.2 - - + -
92F ASN 3.9 1.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il